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  1. Jalview
  2. JAL-3869

Can't run jalview on OS X from command line

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: None
    • Fix Version/s: 2.11.2.6
    • Component/s: None
    • Labels:
      None
    • Environment:
      OS X Catalina, most current java

      Description

      I am trying to obtain consensus sequences from over 100 different alignments using jalview on the command line.
      I installed jalview on conda on 9/8/21 and the installation went fine.
      Here is my input:
      jalview -open GC_00000001_sequences.fa
      Here's what I get back:
      Running jalview.bin.Jalview with memory setting -Xmx15461881856
      Java version: 11.0.9.1
      Java Home: /Users/duerkoplab/opt/miniconda3
      x86_64 Mac OS X 10.15.7
      Jalview Version: 2.11.1.4 (bioconda (build 1) git-commit: [])
      # INFO: Setting default net timeout to 30 seconds.
      VAqua: installed patch for main/key window support
      Exception in thread "main" java.lang.NoClassDefFoundError: sun/awt/image/MultiResolutionImage
      at java.base/java.lang.ClassLoader.defineClass1(Native Method)
      at java.base/java.lang.ClassLoader.defineClass(ClassLoader.java:1017)
      at java.base/java.security.SecureClassLoader.defineClass(SecureClassLoader.java:174)
      at java.base/jdk.internal.loader.BuiltinClassLoader.defineClass(BuiltinClassLoader.java:800)
      at java.base/jdk.internal.loader.BuiltinClassLoader.findClassOnClassPathOrNull(BuiltinClassLoader.java:698)
      at java.base/jdk.internal.loader.BuiltinClassLoader.loadClassOrNull(BuiltinClassLoader.java:621)
      at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:579)
      at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:178)
      at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:522)
      at java.base/java.lang.Class.forName0(Native Method)
      at java.base/java.lang.Class.forName(Class.java:315)
      at org.violetlib.aqua.JavaSupport.findImpl(Unknown Source)
      at org.violetlib.aqua.JavaSupport.<clinit>(Unknown Source)
      at org.violetlib.aqua.AquaLookAndFeel.initialize(Unknown Source)
      at java.desktop/javax.swing.UIManager.setLookAndFeel(UIManager.java:586)
      at java.desktop/javax.swing.UIManager.setLookAndFeel(UIManager.java:633)
      at jalview.bin.Jalview.setSpecificLookAndFeel(Jalview.java:887)
      at jalview.bin.Jalview.setVaquaLookAndFeel(Jalview.java:926)
      at jalview.bin.Jalview.setMacLookAndFeel(Jalview.java:940)
      at jalview.bin.Jalview.setLookAndFeel(Jalview.java:837)
      at jalview.bin.Jalview.doMain(Jalview.java:302)
      at jalview.bin.Jalview.main(Jalview.java:192)
      Caused by: java.lang.ClassNotFoundException: sun.awt.image.MultiResolutionImage
      at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:581)
      at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:178)
      at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:522)
      ... 22 more

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              Assignee:
              soares Ben Soares
              Reporter:
              kirschjo Joshua
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                Created:
                Updated:
                Resolved: